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- PDB-7bkh: 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound... -

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Basic information

Entry
Database: PDB / ID: 7bkh
Title14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-153
Components
  • 14-3-3 protein sigma
  • Transcription factor p65
KeywordsPEPTIDE BINDING PROTEIN / benzaldehyde / covalent fragment / p65 / 1433 / RelA
Function / homology
Function and homology information


acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 ...acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / negative regulation of protein sumoylation / defense response to tumor cell / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to interleukin-6 / Interleukin-1 processing / actinin binding / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / NF-kappaB complex / response to UV-B / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / Regulation of NFE2L2 gene expression / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of miRNA metabolic process / regulation of epidermal cell division / response to cobalamin / protein kinase C inhibitor activity / positive regulation of T cell receptor signaling pathway / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / phosphate ion binding / non-canonical NF-kappaB signal transduction / cellular response to lipoteichoic acid / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / The NLRP3 inflammasome / Regulation of localization of FOXO transcription factors / general transcription initiation factor binding / keratinocyte proliferation / Transcriptional Regulation by VENTX / NF-kappaB binding / hair follicle development / phosphoserine residue binding / neuropeptide signaling pathway / positive regulation of vascular endothelial growth factor production / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / establishment of skin barrier / cellular response to interleukin-1 / response to amino acid / cellular defense response / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Purinergic signaling in leishmaniasis infection / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / response to cAMP / tumor necrosis factor-mediated signaling pathway / protein kinase A signaling / response to muscle stretch / protein export from nucleus / negative regulation of innate immune response / positive regulation of interleukin-12 production / negative regulation of insulin receptor signaling pathway / protein sequestering activity / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / response to interleukin-1 / negative regulation of angiogenesis / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / : / positive regulation of protein export from nucleus / negative regulation of miRNA transcription / liver development / positive regulation of interleukin-1 beta production / response to progesterone / response to cytokine / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / response to ischemia / positive regulation of interleukin-8 production / Dectin-1 mediated noncanonical NF-kB signaling / negative regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / Activation of NF-kappaB in B cells / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding
Similarity search - Function
Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. ...Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-U1B / 14-3-3 protein sigma / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsWolter, M. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179European Union
CitationJournal: J.Med.Chem. / Year: 2021
Title: An Exploration of Chemical Properties Required for Cooperative Stabilization of the 14-3-3 Interaction with NF-kappa B-Utilizing a Reversible Covalent Tethering Approach.
Authors: Wolter, M. / Valenti, D. / Cossar, P.J. / Hristeva, S. / Levy, L.M. / Genski, T. / Hoffmann, T. / Brunsveld, L. / Tzalis, D. / Ottmann, C.
History
DepositionJan 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Transcription factor p65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1394
Polymers29,6392
Non-polymers5012
Water4,864270
1
A: 14-3-3 protein sigma
P: Transcription factor p65
hetero molecules

A: 14-3-3 protein sigma
P: Transcription factor p65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2798
Polymers59,2784
Non-polymers1,0014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4570 Å2
ΔGint-23 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.598, 112.440, 62.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-655-

HOH

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 28226.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Transcription factor p65 / Nuclear factor NF-kappa-B p65 subunit / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3


Mass: 1412.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206
#3: Chemical ChemComp-U1B / 4-nitro-3-[(3S)-3-oxidanylpiperidin-1-yl]benzaldehyde / 4-nitro-3-[(3~{S})-3-oxidanylpiperidin-1-yl]benzaldehyde / 3-(3-hydroxypiperidin-1-yl)-4-nitrobenzaldehyde


Mass: 250.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.91 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.095 M HEPES Na pH 7.1, 27% PEG400, 0.19M Calcium chloride, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→34.49 Å / Num. obs: 56675 / % possible obs: 98.5 % / Redundancy: 13.2 % / Biso Wilson estimate: 15.49 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.053 / Rrim(I) all: 0.193 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.4213.70.5113737827270.9380.1420.5313.796.8
7.67-34.4910.80.09239713660.990.030.09710.790.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Aimless0.7.2data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QHL

6qhl


Resolution: 1.4→34.49 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 2873 5.05 %
Rwork0.1783 103707 -
obs0.1792 56639 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.19 Å2 / Biso mean: 20.8429 Å2 / Biso min: 8.23 Å2
Refinement stepCycle: final / Resolution: 1.4→34.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 35 270 2137
Biso mean--36.05 31.17 -
Num. residues----236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.24441470.22283361350897
1.42-1.430.2221830.22933399358297
1.43-1.450.20261630.22143425358897
1.45-1.470.24791940.20973424361897
1.47-1.490.22242030.20973433363697
1.49-1.510.22561700.19913397356797
1.51-1.530.26331830.21773459364297
1.53-1.550.22391800.19413402358298
1.55-1.580.19662220.19433402362498
1.58-1.60.21661590.18863422358198
1.6-1.630.21421960.19013462365898
1.63-1.660.2451890.1853456364598
1.66-1.690.22612080.17953419362798
1.69-1.730.22261830.18573446362998
1.73-1.760.222020.18423462366498
1.76-1.80.19871610.19233491365299
1.8-1.850.21282060.18153435364199
1.85-1.90.22941690.19363472364199
1.9-1.960.20231990.2023480367999
1.96-2.020.20661880.17523460364899
2.02-2.090.16151880.16883483367199
2.09-2.170.16682050.16213487369299
2.17-2.270.17931880.16493466365499
2.27-2.390.1572150.16053451366699
2.39-2.540.18021760.171335033679100
2.54-2.740.17541610.177135393700100
2.74-3.020.24062000.182635063706100
3.02-3.450.20851530.172835413694100
3.45-4.350.16261590.156935543713100
4.35-34.490.20161640.1873470363498

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